Genome sequencing of SARS-CoV-2 omicron variants in Delhi reveals alterations in immunogenic regions in spike glycoprotein

Figures

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  Figure 1. Phylogenetic analysis of WGS of SARS-CoV-2 along with other variants. NICPR samples are indicated in different colors with highlighted background for visualization with their Omicron subvariants in the same color. The multiple sequence aligned with the MEGA 11 and nexus file was used to construct and visualize the phylogenetic tree (maximum likelihood method) using the iTOL software. Default settings have been used in MEGA 11 and iTOL analysis.

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  Figure 2. Heat map of mutations in spike glycoprotein prevalent in major variants of SARS-CoV-2. Red boxes represent mutation in the SARS-CoV-2 variants and genomes included in the study, blue boxes represent absence of amino acid mutation in the spike glycoprotein. NICPR# represents shared set of mutations in genomes of NICPR1, NICPR4, NICPR5, NICPR6 and NICPR 11. NICPR* represents shared set of mutations in genomes of NICPR2, NICPR3, NICPR7, NICPR8, NICPR9, NICPR10, NICPR12, NICPR14, NICPR15, NICPR16, NICPR17 and NICPR18.

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  Figure 3. The interfacial region of spike protein in cyan and antibody in yellow is shown. Interaction of spike protein’s residue152 before (A) and after mutation (B) to the antibody (PDB ID: 8dls. Interaction of spike protein’s residue G339 with antibody before (C) and after mutation G339H in Delta variant (D) and G339D in omicron variant (E) (PDB ID: 7xsw).

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  Figure 4. Implications of R346T/N mutations in possible immune evasion. (A) the binding of Omicron spike with antibodies specific for class III. (B, C) Loss of this interaction in case of mutation R346T/N with D93 of ACE2 receptor.

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  Figure 5. Interaction of RBD domain of Spike in cyan to ACE-2 Receptor in grey (PDB ID: 6lzg). The interacting residues of RBD domain are shown in orange and interacting residues of ACE-2 receptor are shown in green (N atom in selected residues is shown blue and O atom is shown in red).